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A Compliment to Clinical Testing: Tracking the Coronavirus Through Wastewater

As the United States struggles to ramp up coronavirus testing, an untapped resource flows beneath our feet.

Untapped, that is, until recently. Last month, MIT researchers began testing wastewater in Massachusetts for traces of coronavirus. Now, they’re at work to expand the project, establishing a way to track the virus that would complement current testing. The group, led by Prof. Eric Alm (MIT Department of Biological Engineering), published preliminary work on MedRxiv last week.

The group collected sewage from a major treatment facility between March 18th and the 25th. Right away, the group saw higher concentrations of SARS-CoV-2 than expected, suggesting the number of confirmed cases underestimates the real count. “We were surprised we could say something about the disease prevalence by looking at the data we have.” Alm says. But for now, these are “back of the envelope measurements.”

To poke at the number of people infected, the group plugged variables into an equation. They needed to assume certain things, like the size of a typical stool and the number of people who poop each day.

But one big unknown was the amount of virus that sick people excrete in their stools. Numbers from one study suggest 0.1% of all feces tested positive for SARS-CoV-2 — much higher than 0.026% of the population confirmed in Massachusetts. Another study reported a lower number of viral material per fecal sample - use that estimate, and it raised the prevalence to about 5%, almost two-hundred times higher than the percentage of confirmed cases.

Plugging numbers into an algebraic equation may never be that helpful. Instead, the group is taking a different approach to uncover the relationship between wastewater and the number of infections. To do this, they began sampling sewage from neighborhoods of all sizes. If a neighborhood is small enough, it has a certain chance of having zero cases of COVID-19. The group can analyze these probabilities to come up with a more precise estimate of actual cases.

“Once we figure out that proportionality constant, then I think the data that’s coming out of each of the treatment plants is going to be pretty useful and potentially actionable,” Alm says.

To process the wastewater, the group separates viruses from any larger particles, including bacteria and fecal matter, and then extracts the genetic material. This genetic broth contains fragments of RNA and DNA from innumerable viruses. To single out SARS-CoV-2, the researchers used polymerase chain reaction (PCR) to pump out many copies of the coronavirus RNA, making it detectable.

As the group continues to analyze the data, they may also sequence the DNA of bacteria that has been filtered out. “We all have a few hundred bacterial species living in our guts,” Alm says. Using a machine-learning program developed within the group, they would analyze the types of bacteria present, pinpointing the number of people represented in a given sample.

Alm and the researchers have expanded the project far beyond Massachusetts, working with about 100 wastewater treatment plants across 25 states. The group has sent out devices to be placed directly in manholes for collecting wastewater. They receive samples from each city every week.

Through this work, the group hopes to provide a good complement to traditional testing. Most people who get tested for COVID-19 either show symptoms, or came into contact with someone who tested positive. In contrast, wastewater gives researchers the chance to do random sampling — it’s one shot at getting a bird’s-eye look at the disease.

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